diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0ddf057d60cfb77578f48ea135b663f813c93bb2..35412ae56cfa23d45faad0969ddfcfd8fab1d99c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -9,7 +9,8 @@ cache: - node_modules/ stages: - - pfam + - get-data + - format-data - build - deploy @@ -40,19 +41,33 @@ stages: # when: on_success # expire_in: "30 days" -pfam: +get-pfam: image: ubuntu:23.04 - stage: pfam + stage: get-data before_script: - apt update && apt install -y curl - curl https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz --output pfam-data.gz - ls -al script: - gunzip pfam-data.gz - - ls -al - # artifacts: - # paths: - # - mycv.p + - ls -al pfam-data/ + artifacts: + paths: + - pfam-data/Pfam-A.hmm.dat + +format-pfam: + image: python:3.11 + needs: + - "get-pfam" + before_script: + - pip install pandas + - mv pfam-data/Pfam-A.hmm.dat scripts + script: + - ./scripts/pfam-a-hmm-to-csv.py + - mv ./scripts/Pfam-A.hmm.dat.csv content/_partial/pfam-a-hmm.csv + artifacts: + paths: + - content/_partial/pfam-a-hmm.csv build:dev: extends: .build